Starting phenix.real_space_refine on Thu Feb 15 15:49:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyk_26183/02_2024/7tyk_26183_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyk_26183/02_2024/7tyk_26183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyk_26183/02_2024/7tyk_26183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyk_26183/02_2024/7tyk_26183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyk_26183/02_2024/7tyk_26183_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyk_26183/02_2024/7tyk_26183_neut.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 8034 2.51 5 N 2260 2.21 5 O 2326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12698 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6349 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 44, 'TRANS': 764} Chain breaks: 4 Chain: "B" Number of atoms: 6349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6349 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 44, 'TRANS': 764} Chain breaks: 4 Time building chain proxies: 6.92, per 1000 atoms: 0.54 Number of scatterers: 12698 At special positions: 0 Unit cell: (141.48, 113.4, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 2326 8.00 N 2260 7.00 C 8034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 232 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 274 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS A 631 " - pdb=" SG CYS A 838 " distance=2.03 Simple disulfide: pdb=" SG CYS A 764 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 232 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 274 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 423 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 631 " - pdb=" SG CYS B 838 " distance=2.03 Simple disulfide: pdb=" SG CYS B 764 " - pdb=" SG CYS B 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.94 Conformation dependent library (CDL) restraints added in 2.5 seconds 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 32 sheets defined 11.4% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 removed outlier: 3.770A pdb=" N GLN A 18 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 removed outlier: 3.598A pdb=" N PHE A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.592A pdb=" N ASN A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.521A pdb=" N CYS A 220 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 423 through 435 removed outlier: 4.063A pdb=" N ILE A 427 " --> pdb=" O CYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 678 through 693 removed outlier: 4.024A pdb=" N ASN A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 848 removed outlier: 3.858A pdb=" N PHE A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 removed outlier: 3.769A pdb=" N GLN B 18 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 removed outlier: 3.599A pdb=" N PHE B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.593A pdb=" N ASN B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.520A pdb=" N CYS B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 311 through 316 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 423 through 435 removed outlier: 4.063A pdb=" N ILE B 427 " --> pdb=" O CYS B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 626 Processing helix chain 'B' and resid 678 through 693 removed outlier: 4.024A pdb=" N ASN B 693 " --> pdb=" O ASN B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 848 removed outlier: 3.858A pdb=" N PHE B 847 " --> pdb=" O ARG B 843 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 10 removed outlier: 8.120A pdb=" N GLN A 30 " --> pdb=" O PRO A 5 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 7 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU A 32 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 10 removed outlier: 8.120A pdb=" N GLN A 30 " --> pdb=" O PRO A 5 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 7 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU A 32 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 57 " --> pdb=" O HIS A 28 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLN A 30 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU A 59 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 32 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 61 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 57 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE A 92 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 59 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ARG A 114 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A 90 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLU A 116 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE A 92 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 228 Processing sheet with id=AA5, first strand: chain 'A' and resid 241 through 243 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283 removed outlier: 3.511A pdb=" N HIS A 292 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 309 removed outlier: 7.137A pdb=" N CYS A 302 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N SER A 327 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 304 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N ILE A 329 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N THR A 306 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 309 removed outlier: 7.137A pdb=" N CYS A 302 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N SER A 327 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 304 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N ILE A 329 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N THR A 306 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU A 356 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU A 391 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE A 358 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR A 415 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR A 389 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA A 417 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A 391 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 459 through 460 removed outlier: 6.100A pdb=" N ARG A 459 " --> pdb=" O GLN A 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 463 through 468 removed outlier: 6.632A pdb=" N ARG A 476 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN A 466 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 474 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR A 468 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 518 through 522 Processing sheet with id=AB3, first strand: chain 'A' and resid 583 through 591 removed outlier: 5.926A pdb=" N ASP A 584 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A 600 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN A 590 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 737 through 741 removed outlier: 3.670A pdb=" N TYR A 611 " --> pdb=" O CYS A 764 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU A 756 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 797 through 800 Processing sheet with id=AB6, first strand: chain 'A' and resid 835 through 840 removed outlier: 7.219A pdb=" N THR A 867 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 835 through 840 Processing sheet with id=AB8, first strand: chain 'B' and resid 5 through 10 removed outlier: 8.121A pdb=" N GLN B 30 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 7 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU B 32 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET B 34 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 5 through 10 removed outlier: 8.121A pdb=" N GLN B 30 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 7 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU B 32 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET B 34 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU B 57 " --> pdb=" O HIS B 28 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLN B 30 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 59 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 32 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG B 61 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 57 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE B 92 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 59 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ARG B 114 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 90 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLU B 116 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE B 92 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AC2, first strand: chain 'B' and resid 226 through 228 Processing sheet with id=AC3, first strand: chain 'B' and resid 241 through 243 Processing sheet with id=AC4, first strand: chain 'B' and resid 282 through 283 removed outlier: 3.511A pdb=" N HIS B 292 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 301 through 309 removed outlier: 7.136A pdb=" N CYS B 302 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER B 327 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 304 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N ILE B 329 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N THR B 306 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 301 through 309 removed outlier: 7.136A pdb=" N CYS B 302 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER B 327 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 304 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N ILE B 329 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N THR B 306 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU B 356 " --> pdb=" O TYR B 389 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU B 391 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE B 358 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR B 415 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR B 389 " --> pdb=" O TYR B 415 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA B 417 " --> pdb=" O TYR B 389 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B 391 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 459 through 460 removed outlier: 6.100A pdb=" N ARG B 459 " --> pdb=" O GLN B 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 463 through 468 removed outlier: 6.631A pdb=" N ARG B 476 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN B 466 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 474 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR B 468 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 518 through 522 Processing sheet with id=AD1, first strand: chain 'B' and resid 583 through 591 removed outlier: 5.925A pdb=" N ASP B 584 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS B 600 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN B 590 " --> pdb=" O HIS B 594 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS B 594 " --> pdb=" O ASN B 590 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 737 through 741 removed outlier: 3.671A pdb=" N TYR B 611 " --> pdb=" O CYS B 764 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU B 756 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 797 through 800 Processing sheet with id=AD4, first strand: chain 'B' and resid 835 through 840 removed outlier: 7.219A pdb=" N THR B 867 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 835 through 840 282 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.24: 1729 1.24 - 1.55: 11175 1.55 - 1.86: 94 1.86 - 2.17: 0 2.17 - 2.48: 2 Bond restraints: 13000 Sorted by residual: bond pdb=" CB PRO A 136 " pdb=" CG PRO A 136 " ideal model delta sigma weight residual 1.492 2.479 -0.987 5.00e-02 4.00e+02 3.90e+02 bond pdb=" CB PRO B 136 " pdb=" CG PRO B 136 " ideal model delta sigma weight residual 1.492 2.479 -0.987 5.00e-02 4.00e+02 3.90e+02 bond pdb=" CG PRO B 136 " pdb=" CD PRO B 136 " ideal model delta sigma weight residual 1.503 0.930 0.573 3.40e-02 8.65e+02 2.84e+02 bond pdb=" CG PRO A 136 " pdb=" CD PRO A 136 " ideal model delta sigma weight residual 1.503 0.930 0.573 3.40e-02 8.65e+02 2.84e+02 bond pdb=" CG PRO B 482 " pdb=" CD PRO B 482 " ideal model delta sigma weight residual 1.503 1.143 0.360 3.40e-02 8.65e+02 1.12e+02 ... (remaining 12995 not shown) Histogram of bond angle deviations from ideal: 0.01 - 29.72: 2 29.72 - 59.42: 0 59.42 - 89.13: 6 89.13 - 118.83: 10560 118.83 - 148.54: 7104 Bond angle restraints: 17672 Sorted by residual: angle pdb=" CB PRO B 136 " pdb=" CG PRO B 136 " pdb=" CD PRO B 136 " ideal model delta sigma weight residual 106.10 0.01 106.09 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CB PRO A 136 " pdb=" CG PRO A 136 " pdb=" CD PRO A 136 " ideal model delta sigma weight residual 106.10 0.03 106.07 3.20e+00 9.77e-02 1.10e+03 angle pdb=" N PRO A 482 " pdb=" CD PRO A 482 " pdb=" CG PRO A 482 " ideal model delta sigma weight residual 103.20 77.23 25.97 1.50e+00 4.44e-01 3.00e+02 angle pdb=" N PRO B 482 " pdb=" CD PRO B 482 " pdb=" CG PRO B 482 " ideal model delta sigma weight residual 103.20 77.26 25.94 1.50e+00 4.44e-01 2.99e+02 angle pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " pdb=" CG PRO B 482 " ideal model delta sigma weight residual 104.50 74.57 29.93 1.90e+00 2.77e-01 2.48e+02 ... (remaining 17667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.64: 7363 29.64 - 59.28: 419 59.28 - 88.92: 56 88.92 - 118.56: 1 118.56 - 148.20: 1 Dihedral angle restraints: 7840 sinusoidal: 3170 harmonic: 4670 Sorted by residual: dihedral pdb=" N PRO B 136 " pdb=" CG PRO B 136 " pdb=" CD PRO B 136 " pdb=" CB PRO B 136 " ideal model delta sinusoidal sigma weight residual 30.00 178.20 -148.20 1 1.50e+01 4.44e-03 7.89e+01 dihedral pdb=" CB CYS A 165 " pdb=" SG CYS A 165 " pdb=" SG CYS A 184 " pdb=" CB CYS A 184 " ideal model delta sinusoidal sigma weight residual -86.00 -161.75 75.75 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CB CYS B 165 " pdb=" SG CYS B 165 " pdb=" SG CYS B 184 " pdb=" CB CYS B 184 " ideal model delta sinusoidal sigma weight residual -86.00 -161.71 75.71 1 1.00e+01 1.00e-02 7.23e+01 ... (remaining 7837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1289 0.032 - 0.064: 443 0.064 - 0.096: 120 0.096 - 0.128: 106 0.128 - 0.160: 10 Chirality restraints: 1968 Sorted by residual: chirality pdb=" CA PRO A 136 " pdb=" N PRO A 136 " pdb=" C PRO A 136 " pdb=" CB PRO A 136 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CA PRO B 136 " pdb=" N PRO B 136 " pdb=" C PRO B 136 " pdb=" CB PRO B 136 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ILE B 91 " pdb=" N ILE B 91 " pdb=" C ILE B 91 " pdb=" CB ILE B 91 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 1965 not shown) Planarity restraints: 2296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 482 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.89e+00 pdb=" C PRO A 482 " -0.045 2.00e-02 2.50e+03 pdb=" O PRO A 482 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 483 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 482 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C PRO B 482 " 0.045 2.00e-02 2.50e+03 pdb=" O PRO B 482 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU B 483 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 135 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C ALA B 135 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA B 135 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO B 136 " 0.014 2.00e-02 2.50e+03 ... (remaining 2293 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 729 2.73 - 3.27: 12103 3.27 - 3.82: 19660 3.82 - 4.36: 23600 4.36 - 4.90: 41473 Nonbonded interactions: 97565 Sorted by model distance: nonbonded pdb=" O HIS B 766 " pdb=" OG1 THR B 770 " model vdw 2.189 2.440 nonbonded pdb=" O HIS A 766 " pdb=" OG1 THR A 770 " model vdw 2.190 2.440 nonbonded pdb=" O LEU A 461 " pdb=" OG SER A 567 " model vdw 2.264 2.440 nonbonded pdb=" O SER A 265 " pdb=" NH2 ARG A 284 " model vdw 2.264 2.520 nonbonded pdb=" O SER B 265 " pdb=" NH2 ARG B 284 " model vdw 2.264 2.520 ... (remaining 97560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.850 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 37.400 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.987 13000 Z= 1.211 Angle : 1.391 106.088 17672 Z= 0.583 Chirality : 0.042 0.160 1968 Planarity : 0.003 0.034 2296 Dihedral : 17.403 148.196 4736 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.51 % Favored : 91.11 % Rotamer: Outliers : 0.65 % Allowed : 23.37 % Favored : 75.98 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.21), residues: 1598 helix: 1.31 (0.50), residues: 132 sheet: -0.35 (0.25), residues: 432 loop : -1.86 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 179 HIS 0.006 0.001 HIS B 762 PHE 0.012 0.001 PHE B 548 TYR 0.008 0.001 TYR A 56 ARG 0.003 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 118 average time/residue: 0.2626 time to fit residues: 45.2508 Evaluate side-chains 114 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain B residue 371 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN A 689 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN B 689 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.0527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13000 Z= 0.183 Angle : 0.545 11.548 17672 Z= 0.281 Chirality : 0.043 0.138 1968 Planarity : 0.004 0.088 2296 Dihedral : 4.306 23.311 1782 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.95 % Favored : 90.68 % Rotamer: Outliers : 2.90 % Allowed : 23.08 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.21), residues: 1598 helix: 1.30 (0.52), residues: 132 sheet: -0.44 (0.25), residues: 430 loop : -1.87 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 616 HIS 0.005 0.001 HIS B 762 PHE 0.014 0.001 PHE A 548 TYR 0.011 0.001 TYR B 494 ARG 0.002 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 124 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 LYS cc_start: 0.7866 (mtmm) cc_final: 0.7627 (mmmm) REVERT: A 520 LEU cc_start: 0.8616 (tt) cc_final: 0.8387 (tp) REVERT: B 371 LYS cc_start: 0.7856 (mtmm) cc_final: 0.7617 (mmmm) REVERT: B 520 LEU cc_start: 0.8605 (tt) cc_final: 0.8372 (tp) outliers start: 40 outliers final: 13 residues processed: 162 average time/residue: 0.2358 time to fit residues: 56.6933 Evaluate side-chains 128 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 819 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 0.4980 chunk 157 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS A 466 ASN A 628 ASN A 689 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN B 628 ASN B 689 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13000 Z= 0.331 Angle : 0.604 6.100 17672 Z= 0.312 Chirality : 0.045 0.148 1968 Planarity : 0.004 0.031 2296 Dihedral : 4.836 22.600 1772 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.95 % Favored : 88.67 % Rotamer: Outliers : 5.37 % Allowed : 21.04 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.21), residues: 1598 helix: 0.86 (0.50), residues: 134 sheet: -0.58 (0.25), residues: 430 loop : -1.94 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 616 HIS 0.007 0.001 HIS A 762 PHE 0.018 0.002 PHE B 548 TYR 0.017 0.002 TYR B 389 ARG 0.003 0.000 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 107 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 HIS cc_start: 0.7138 (m90) cc_final: 0.6844 (m170) REVERT: A 213 GLN cc_start: 0.7737 (mp10) cc_final: 0.7319 (mm110) REVERT: A 344 HIS cc_start: 0.6997 (OUTLIER) cc_final: 0.6401 (t70) REVERT: A 641 ASN cc_start: 0.7946 (t0) cc_final: 0.7402 (t0) REVERT: A 766 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.4808 (m90) REVERT: B 192 HIS cc_start: 0.7140 (m90) cc_final: 0.6846 (m170) REVERT: B 213 GLN cc_start: 0.7679 (mp10) cc_final: 0.7300 (mm110) REVERT: B 520 LEU cc_start: 0.8958 (tt) cc_final: 0.8725 (tp) REVERT: B 641 ASN cc_start: 0.7946 (t0) cc_final: 0.7396 (t0) REVERT: B 766 HIS cc_start: 0.6688 (OUTLIER) cc_final: 0.4862 (m90) outliers start: 74 outliers final: 43 residues processed: 177 average time/residue: 0.2492 time to fit residues: 64.7907 Evaluate side-chains 150 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 104 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 847 PHE Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS A 689 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS B 628 ASN B 689 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13000 Z= 0.398 Angle : 0.641 7.667 17672 Z= 0.332 Chirality : 0.046 0.157 1968 Planarity : 0.005 0.030 2296 Dihedral : 5.160 23.816 1772 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.14 % Favored : 87.48 % Rotamer: Outliers : 5.81 % Allowed : 22.50 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.21), residues: 1598 helix: 0.51 (0.49), residues: 134 sheet: -0.62 (0.26), residues: 430 loop : -2.03 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 542 HIS 0.009 0.002 HIS A 344 PHE 0.019 0.002 PHE A 548 TYR 0.019 0.002 TYR B 389 ARG 0.003 0.000 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 95 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 HIS cc_start: 0.7246 (m90) cc_final: 0.6779 (m170) REVERT: A 213 GLN cc_start: 0.7809 (mp10) cc_final: 0.7499 (mm110) REVERT: A 344 HIS cc_start: 0.6820 (OUTLIER) cc_final: 0.6431 (t70) REVERT: A 641 ASN cc_start: 0.8001 (t0) cc_final: 0.7444 (t0) REVERT: A 766 HIS cc_start: 0.7011 (OUTLIER) cc_final: 0.4857 (m90) REVERT: B 192 HIS cc_start: 0.7250 (m90) cc_final: 0.6781 (m170) REVERT: B 213 GLN cc_start: 0.7801 (mp10) cc_final: 0.7495 (mm110) REVERT: B 344 HIS cc_start: 0.6946 (OUTLIER) cc_final: 0.6423 (t70) REVERT: B 641 ASN cc_start: 0.7992 (t0) cc_final: 0.7435 (t0) REVERT: B 766 HIS cc_start: 0.7058 (OUTLIER) cc_final: 0.4892 (m90) outliers start: 80 outliers final: 47 residues processed: 171 average time/residue: 0.2306 time to fit residues: 58.7458 Evaluate side-chains 145 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 94 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 344 HIS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 847 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.0270 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 0 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS A 628 ASN A 689 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN B 344 HIS B 689 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13000 Z= 0.185 Angle : 0.542 6.287 17672 Z= 0.282 Chirality : 0.043 0.138 1968 Planarity : 0.004 0.031 2296 Dihedral : 4.777 23.233 1772 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.57 % Favored : 90.05 % Rotamer: Outliers : 4.79 % Allowed : 23.37 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.22), residues: 1598 helix: 0.81 (0.51), residues: 134 sheet: -0.55 (0.26), residues: 430 loop : -1.92 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 179 HIS 0.010 0.001 HIS A 344 PHE 0.013 0.001 PHE A 548 TYR 0.015 0.001 TYR B 630 ARG 0.001 0.000 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 105 time to evaluate : 1.388 Fit side-chains REVERT: A 192 HIS cc_start: 0.6888 (m90) cc_final: 0.6524 (m170) REVERT: A 213 GLN cc_start: 0.7807 (mp10) cc_final: 0.7471 (mm110) REVERT: A 520 LEU cc_start: 0.8926 (tt) cc_final: 0.8720 (tp) REVERT: A 628 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7958 (p0) REVERT: A 641 ASN cc_start: 0.7991 (t0) cc_final: 0.7399 (t0) REVERT: A 684 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6701 (mt0) REVERT: A 766 HIS cc_start: 0.6902 (OUTLIER) cc_final: 0.4800 (m90) REVERT: B 192 HIS cc_start: 0.6890 (m90) cc_final: 0.6524 (m170) REVERT: B 213 GLN cc_start: 0.7805 (mp10) cc_final: 0.7469 (mm110) REVERT: B 641 ASN cc_start: 0.7981 (t0) cc_final: 0.7391 (t0) REVERT: B 684 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6686 (mt0) REVERT: B 766 HIS cc_start: 0.6963 (OUTLIER) cc_final: 0.4859 (m90) outliers start: 66 outliers final: 32 residues processed: 166 average time/residue: 0.2348 time to fit residues: 57.9712 Evaluate side-chains 132 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 95 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 847 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS A 225 HIS ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS A 628 ASN A 689 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 344 HIS B 689 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13000 Z= 0.209 Angle : 0.545 5.804 17672 Z= 0.283 Chirality : 0.043 0.139 1968 Planarity : 0.004 0.031 2296 Dihedral : 4.665 23.024 1772 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.51 % Favored : 89.11 % Rotamer: Outliers : 5.15 % Allowed : 23.08 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.22), residues: 1598 helix: 0.85 (0.51), residues: 134 sheet: -0.53 (0.26), residues: 430 loop : -1.89 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 179 HIS 0.004 0.001 HIS B 762 PHE 0.016 0.001 PHE A 290 TYR 0.011 0.001 TYR B 389 ARG 0.001 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 101 time to evaluate : 1.600 Fit side-chains REVERT: A 192 HIS cc_start: 0.6795 (m90) cc_final: 0.6449 (m170) REVERT: A 213 GLN cc_start: 0.7758 (mp10) cc_final: 0.7506 (mm110) REVERT: A 344 HIS cc_start: 0.6779 (OUTLIER) cc_final: 0.6428 (t70) REVERT: A 628 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7833 (p0) REVERT: A 641 ASN cc_start: 0.7982 (t0) cc_final: 0.7370 (t0) REVERT: A 684 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6688 (mt0) REVERT: A 766 HIS cc_start: 0.6897 (OUTLIER) cc_final: 0.4781 (m90) REVERT: B 192 HIS cc_start: 0.6795 (m90) cc_final: 0.6450 (m170) REVERT: B 213 GLN cc_start: 0.7751 (mp10) cc_final: 0.7502 (mm110) REVERT: B 344 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.6403 (t70) REVERT: B 641 ASN cc_start: 0.7970 (t0) cc_final: 0.7364 (t0) REVERT: B 684 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6676 (mt0) REVERT: B 766 HIS cc_start: 0.6925 (OUTLIER) cc_final: 0.4802 (m90) outliers start: 71 outliers final: 42 residues processed: 167 average time/residue: 0.2369 time to fit residues: 58.5649 Evaluate side-chains 143 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 94 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 344 HIS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 847 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS A 628 ASN A 689 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS B 628 ASN B 689 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13000 Z= 0.359 Angle : 0.613 5.801 17672 Z= 0.318 Chirality : 0.045 0.155 1968 Planarity : 0.004 0.030 2296 Dihedral : 5.010 23.405 1772 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.33 % Favored : 87.42 % Rotamer: Outliers : 4.93 % Allowed : 24.38 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.21), residues: 1598 helix: 0.68 (0.50), residues: 134 sheet: -0.59 (0.26), residues: 430 loop : -2.02 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 179 HIS 0.018 0.002 HIS A 344 PHE 0.017 0.002 PHE B 548 TYR 0.017 0.002 TYR B 389 ARG 0.003 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 102 time to evaluate : 1.525 Fit side-chains REVERT: A 192 HIS cc_start: 0.7068 (m90) cc_final: 0.6670 (m170) REVERT: A 213 GLN cc_start: 0.7873 (mp10) cc_final: 0.7578 (mm110) REVERT: A 478 GLU cc_start: 0.8336 (pm20) cc_final: 0.8035 (pm20) REVERT: A 641 ASN cc_start: 0.8061 (t0) cc_final: 0.7475 (t0) REVERT: A 684 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6749 (mt0) REVERT: A 766 HIS cc_start: 0.7141 (OUTLIER) cc_final: 0.4853 (m90) REVERT: B 192 HIS cc_start: 0.7070 (m90) cc_final: 0.6676 (m170) REVERT: B 213 GLN cc_start: 0.7882 (mp10) cc_final: 0.7577 (mm110) REVERT: B 478 GLU cc_start: 0.8334 (pm20) cc_final: 0.8038 (pm20) REVERT: B 641 ASN cc_start: 0.8049 (t0) cc_final: 0.7466 (t0) REVERT: B 684 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6737 (mt0) REVERT: B 766 HIS cc_start: 0.7224 (OUTLIER) cc_final: 0.4896 (m90) outliers start: 68 outliers final: 50 residues processed: 165 average time/residue: 0.2357 time to fit residues: 57.6189 Evaluate side-chains 152 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 98 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 847 PHE Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN A 689 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN B 689 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13000 Z= 0.219 Angle : 0.556 5.278 17672 Z= 0.288 Chirality : 0.043 0.143 1968 Planarity : 0.004 0.031 2296 Dihedral : 4.812 23.394 1772 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.08 % Favored : 89.67 % Rotamer: Outliers : 5.44 % Allowed : 24.17 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.22), residues: 1598 helix: 0.82 (0.50), residues: 134 sheet: -0.54 (0.26), residues: 430 loop : -1.98 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 179 HIS 0.004 0.001 HIS B 762 PHE 0.018 0.001 PHE A 290 TYR 0.012 0.001 TYR A 389 ARG 0.004 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 103 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 HIS cc_start: 0.7031 (m90) cc_final: 0.6664 (m170) REVERT: A 213 GLN cc_start: 0.7814 (mp10) cc_final: 0.7548 (mm110) REVERT: A 478 GLU cc_start: 0.8352 (pm20) cc_final: 0.8102 (pm20) REVERT: A 641 ASN cc_start: 0.8027 (t0) cc_final: 0.7403 (t0) REVERT: A 684 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6700 (mt0) REVERT: A 766 HIS cc_start: 0.7085 (OUTLIER) cc_final: 0.4868 (m90) REVERT: B 192 HIS cc_start: 0.7033 (m90) cc_final: 0.6654 (m170) REVERT: B 213 GLN cc_start: 0.7808 (mp10) cc_final: 0.7548 (mm110) REVERT: B 478 GLU cc_start: 0.8345 (pm20) cc_final: 0.8065 (pm20) REVERT: B 641 ASN cc_start: 0.8012 (t0) cc_final: 0.7402 (t0) REVERT: B 684 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6691 (mt0) REVERT: B 766 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.4925 (m90) outliers start: 75 outliers final: 57 residues processed: 176 average time/residue: 0.2271 time to fit residues: 59.2987 Evaluate side-chains 159 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 98 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain A residue 872 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 847 PHE Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13000 Z= 0.202 Angle : 0.551 8.524 17672 Z= 0.283 Chirality : 0.043 0.140 1968 Planarity : 0.004 0.031 2296 Dihedral : 4.690 23.159 1772 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.64 % Favored : 89.11 % Rotamer: Outliers : 5.08 % Allowed : 24.38 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.22), residues: 1598 helix: 0.92 (0.50), residues: 134 sheet: -0.53 (0.26), residues: 430 loop : -1.96 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 179 HIS 0.004 0.001 HIS A 762 PHE 0.013 0.001 PHE A 548 TYR 0.011 0.001 TYR A 389 ARG 0.004 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 107 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 HIS cc_start: 0.6901 (m90) cc_final: 0.6684 (m170) REVERT: A 213 GLN cc_start: 0.7819 (mp10) cc_final: 0.7579 (mm110) REVERT: A 348 LEU cc_start: 0.8387 (mm) cc_final: 0.8103 (mt) REVERT: A 478 GLU cc_start: 0.8345 (pm20) cc_final: 0.8096 (pm20) REVERT: A 641 ASN cc_start: 0.7995 (t0) cc_final: 0.7373 (t0) REVERT: A 684 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6637 (mt0) REVERT: A 766 HIS cc_start: 0.7058 (OUTLIER) cc_final: 0.4726 (m90) REVERT: B 192 HIS cc_start: 0.6902 (m90) cc_final: 0.6686 (m170) REVERT: B 213 GLN cc_start: 0.7817 (mp10) cc_final: 0.7581 (mm110) REVERT: B 348 LEU cc_start: 0.8373 (mm) cc_final: 0.8099 (mt) REVERT: B 478 GLU cc_start: 0.8333 (pm20) cc_final: 0.8065 (pm20) REVERT: B 641 ASN cc_start: 0.7995 (t0) cc_final: 0.7376 (t0) REVERT: B 684 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6629 (mt0) REVERT: B 766 HIS cc_start: 0.7126 (OUTLIER) cc_final: 0.4786 (m90) outliers start: 70 outliers final: 57 residues processed: 174 average time/residue: 0.2349 time to fit residues: 60.6937 Evaluate side-chains 163 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 102 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain A residue 872 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 847 PHE Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 8.9990 chunk 92 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13000 Z= 0.287 Angle : 0.590 7.902 17672 Z= 0.304 Chirality : 0.045 0.150 1968 Planarity : 0.004 0.033 2296 Dihedral : 4.864 23.463 1772 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.58 % Favored : 88.17 % Rotamer: Outliers : 4.64 % Allowed : 24.53 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.22), residues: 1598 helix: 0.82 (0.50), residues: 134 sheet: -0.57 (0.27), residues: 426 loop : -2.00 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 179 HIS 0.006 0.001 HIS A 766 PHE 0.019 0.002 PHE B 290 TYR 0.015 0.001 TYR B 389 ARG 0.004 0.000 ARG B 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 101 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 HIS cc_start: 0.7020 (m90) cc_final: 0.6791 (m170) REVERT: A 213 GLN cc_start: 0.7830 (mp10) cc_final: 0.7609 (mm110) REVERT: A 348 LEU cc_start: 0.8495 (mm) cc_final: 0.8220 (mt) REVERT: A 478 GLU cc_start: 0.8374 (pm20) cc_final: 0.8082 (pm20) REVERT: A 641 ASN cc_start: 0.8027 (t0) cc_final: 0.7405 (t0) REVERT: A 684 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6717 (mt0) REVERT: A 766 HIS cc_start: 0.7115 (OUTLIER) cc_final: 0.4770 (m90) REVERT: B 192 HIS cc_start: 0.7019 (m90) cc_final: 0.6792 (m170) REVERT: B 213 GLN cc_start: 0.7826 (mp10) cc_final: 0.7607 (mm110) REVERT: B 348 LEU cc_start: 0.8493 (mm) cc_final: 0.8207 (mt) REVERT: B 478 GLU cc_start: 0.8346 (pm20) cc_final: 0.8064 (pm20) REVERT: B 641 ASN cc_start: 0.8027 (t0) cc_final: 0.7405 (t0) REVERT: B 684 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6708 (mt0) REVERT: B 766 HIS cc_start: 0.7139 (OUTLIER) cc_final: 0.4787 (m90) outliers start: 64 outliers final: 56 residues processed: 163 average time/residue: 0.2278 time to fit residues: 55.6929 Evaluate side-chains 161 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 101 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain A residue 872 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 847 PHE Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.167133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134025 restraints weight = 16613.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.131891 restraints weight = 16510.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.134091 restraints weight = 15467.403| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.217 13000 Z= 0.343 Angle : 0.878 59.156 17672 Z= 0.515 Chirality : 0.046 0.582 1968 Planarity : 0.005 0.156 2296 Dihedral : 4.853 23.486 1772 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.64 % Favored : 88.11 % Rotamer: Outliers : 4.72 % Allowed : 24.46 % Favored : 70.83 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.22), residues: 1598 helix: 0.84 (0.50), residues: 134 sheet: -0.58 (0.27), residues: 426 loop : -1.99 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 179 HIS 0.006 0.001 HIS A 766 PHE 0.017 0.002 PHE B 290 TYR 0.015 0.001 TYR A 389 ARG 0.003 0.000 ARG B 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2408.77 seconds wall clock time: 44 minutes 36.58 seconds (2676.58 seconds total)